when I go to export the files "same as source," it tries to convert them to the codec that the timeline is in
That's why we often recommend you never use that export setting.
With few exception, PP will transcode upon export. Everything QuickTime will be transcoded, regardless of changes made. This has to do with the 32 bit nature of the QuickTime API and the 'band-aid' Adobe has to implement to make them work in 64 bit Premiere Pro. (This is one reason I recommend against using anything QuickTime if you can avoid it.)
What are the hardware specs and drive setup of your system?